[ensembl-dev] Homology
Javier Herrero
jherrero at ebi.ac.uk
Wed Nov 16 19:33:02 GMT 2011
Hi James
Sorry, I thought BioMart would have solved your problem. I guess it
would be easier it we stick to just one script rather than the two you
mentioned in an earlier email. I think I would opt for the first one
(slides) as the other ones seems a little outdated (from the list).
So, the script from the slides works out of the box (copy & paste from
your email) for me, using e64 API.
It also works if I substitute the gene stable ID by ENSDARG00000090113.
However, if I use a non-existent gene stable ID or anything different
from the gene stable ID, I get the error you reported in another email:
/Can't call method "dbID" on an undefined value at
~/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm
line 37./
Please, use that script and check that it works (with the original gene
identifier). Then change the identifier to get the data for your gene of
interest and check that it still works.
If you get a failure with the original script, there is something wrong
with your setup (API installation, access to the database, etc). If you
get a failure using a different gene identifier, then you are using a
invalid gene identifier.
I hope this helps
Javier
On 16/11/11 18:13, James Blackshaw wrote:
> Hello,
>
> Just a bit of a bump on this as I can't get the script to work and
> I've checked that I am using version 64 of Homologene. I could really
> do with a decent way to get homologs for a given species out of
> Ensembl for a list of genes. Sadly Biomart isn't much use as I cant
> get homologs from yeast or mouse to plants, they're on separate
> filters. Does anyone on this list have a similar script they might be
> willing to send me to see if I can get it to return anything?
>
> Regards,
> James
>>>> Hi,
>>>> this still doesn't work, I get the error:
>>>> "Can't call method "fetch_by_source_stable_id" on an undefined
>>>> value at homology_workshop_getAllHomologuesForGene.pl line 28."
>>>>
>>>> I get the following error off the script for comparing all homologs
>>>> between two species. A pity, as that is otherwise perfect for what
>>>> I want.
>>>> "Can't call method "get_HomologyAdaptor" on an undefined value at
>>>> homology_getAllHomologuesBetween2Species.pl line 24."
>>>>
>>>> Is there anywhere I'd be able to check the version number of the
>>>> API I have?
>>>>
>>>> Regards,
>>>> -James
>>>>
>>>> On 14/11/2011 12:02, Matthieu Muffato wrote:
>>>>> Hi James
>>>>>
>>>>> I just hope there is no misunderstanding with the line numbers.
>>>>> Your script seems to work well, at least here, replacing the
>>>>> $homology_adaptor->fetch_all_by_Member($member) line by
>>>>> $homology_adaptor->fetch_all_by_Member($member->gene_member)
>>>>>
>>>>> I can have the "dbID" error message when applying both changes.
>>>>> They are actually not compatible. Either you specify the gene ID
>>>>> in the first place, and stick with
>>>>> $homology_adaptor->fetch_all_by_Member($member), or you keep the
>>>>> protein ID, and you add the "->gene_member"
>>>>>
>>>>> There is a script in the scripts/examples directory of the
>>>>> ensembl-compara repository, named
>>>>> homology_workshop_getAllHomologuesForGene.pl, that does the job if
>>>>> you know the gene name.
>>>>>
>>>>> Regards,
>>>>> Matthieu
>>>>>
>>>>> On 14/11/11 11:41, James Blackshaw wrote:
>>>>>> Hi Matthieu,
>>>>>> Changing Line 16 doesn't help, I get the same error reported.
>>>>>> Changing line 25 gives me a new error though.
>>>>>> Can't call method "dbID" on an undefined value at
>>>>>> /usr/mbu/software/ensembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm
>>>>>>
>>>>>> line 37.
>>>>>>
>>>>>> What I'm trying to do is get the homologs for a list of proteins or
>>>>>> associated genes, either works. I'm surprised there's not already a
>>>>>> script about for it, but can't find on on the mailing list.
>>>>>>
>>>>>> -James
>>>>>>
>>>>>>
>>>>>> On 14/11/2011 11:25, Matthieu Muffato wrote:
>>>>>>> Hi James
>>>>>>>
>>>>>>> In Comparam the homologies are stored at the gene level. Because
>>>>>>> your
>>>>>>> Member object represents a peptide, the homology list that you
>>>>>>> retrieve is empty.
>>>>>>>
>>>>>>> You can either change the line 25 to
>>>>>>> my $homologies =
>>>>>>> $homology_adaptor->fetch_all_by_Member($member->gene_member);
>>>>>>>
>>>>>>> or change the line 16 to
>>>>>>> my $member =
>>>>>>> $member_adaptor->fetch_by_source_stable_id("ENSEMBLGENE",
>>>>>>> ****) with an Ensembl gene ID if you know it
>>>>>>>
>>>>>>> to have all the homologies of your favourite gene
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>> Matthieu
>>>>>>>
>>>>>>> On 14/11/11 11:15, James Blackshaw wrote:
>>>>>>>> Hi,
>>>>>>>> I am using the code from the API installation page and that
>>>>>>>> page talks
>>>>>>>> about version 64.
>>>>>>>> http://www.ensembl.org/info/docs/api/api_installation.html
>>>>>>>>
>>>>>>>> This is my output under verbose, looks like it is connecting.
>>>>>>>> Odd number of elements in hash assignment at
>>>>>>>> /usr/mbu/software/ensembl/ensembl/modules/Bio/EnsEMBL/Utils/Argument.pm
>>>>>>>>
>>>>>>>> line 148.
>>>>>>>> Transcript:ENSDART00000112153 Gene:ENSDARG00000090113 Chr:19
>>>>>>>> Start:33519855 End:33522332
>>>>>>>> Can't call method "get_all_Member_Attribute" on an undefined
>>>>>>>> value at
>>>>>>>> sandbox3.pl line 47.
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>> James
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11/11/2011 20:20, Javier Herrero wrote:
>>>>>>>>> Hi James
>>>>>>>>>
>>>>>>>>> This error is typical when you fail to connect to the database.
>>>>>>>>>
>>>>>>>>> I suspect you are using the HEAD code instead of the branch
>>>>>>>>> 64. The
>>>>>>>>> head code is already configured for connecting to the forthcoming
>>>>>>>>> database. Please switch your code to the 64 branch and try again:
>>>>>>>>>
>>>>>>>>> cvs up -r branch-ensembl-64
>>>>>>>>>
>>>>>>>>> Regards
>>>>>>>>>
>>>>>>>>> Javier
>>>>>>>>>
>>>>>>>>> On 11/11/11 19:29, Jan Vogel wrote:
>>>>>>>>>> Hi James,
>>>>>>>>>>
>>>>>>>>>> the first script from the powerpoint works for me w/o
>>>>>>>>>> problems or
>>>>>>>>>> modifications. I've tried schema 62 and schema 64 API's.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> The second one ( 'from the list' ) had some minor problems.
>>>>>>>>>> It works
>>>>>>>>>> like this :
>>>>>>>>>>
>>>>>>>>>> my $member =
>>>>>>>>>> $member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','ENSG00000004059');
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> or
>>>>>>>>>>
>>>>>>>>>> my $member =
>>>>>>>>>> $member_adaptor->fetch_by_source_stable_id(undef,'ENSG00000004059');
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I did not try the zfish protein.
>>>>>>>>>>
>>>>>>>>>> Hth,
>>>>>>>>>> Jan
>>>>>>>>>>
>>>>>>>>>> On Nov 11, 2011, at 9:50 AM, James Blackshaw wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>> I've been trying to put together some scripts for finding the
>>>>>>>>>>> homolgies
>>>>>>>>>>> for some lists of genes I'm interested in, but I keep
>>>>>>>>>>> getting errors
>>>>>>>>>>> with the "fetch" methods.
>>>>>>>>>>>
>>>>>>>>>>> "Can't call method "fetch_by_source_stable_id" on an undefined
>>>>>>>>>>> value at
>>>>>>>>>>> sandbox3.pl<http://sandbox3.pl/> line 15."
>>>>>>>>>>>
>>>>>>>>>>> I've used one script taken from a presentation by Stephen
>>>>>>>>>>> Fitzgerald at
>>>>>>>>>>> Edinburgh, and another from this maining list. I'm including
>>>>>>>>>>> both.
>>>>>>>>>>>
>>>>>>>>>>> From the powerpoint:
>>>>>>>>>>> use strict;
>>>>>>>>>>> use Bio::EnsEMBL::Registry;
>>>>>>>>>>> my $reg = "Bio::EnsEMBL::Registry";
>>>>>>>>>>>
>>>>>>>>>>> $reg->load_registry_from_db(
>>>>>>>>>>> -host=>"ensembldb.ensembl.org<http://ensembldb.ensembl.org/>",
>>>>>>>>>>> -user => "anonymous");
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> my $ma = $reg->get_adaptor(
>>>>>>>>>>> "Multi", "compara", "Member");
>>>>>>>>>>> my $member = $ma->fetch_by_source_stable_id(
>>>>>>>>>>> "ENSEMBLGENE", "ENSG00000000971");
>>>>>>>>>>>
>>>>>>>>>>> my $homology_adaptor = $reg->get_adaptor(
>>>>>>>>>>> "Multi", "compara", "Homology");
>>>>>>>>>>>
>>>>>>>>>>> my $homologies = $homology_adaptor->
>>>>>>>>>>> fetch_all_by_Member($member);
>>>>>>>>>>>
>>>>>>>>>>> foreach my $this_homology (@$homologies) {
>>>>>>>>>>> print $this_homology->description, "\n";
>>>>>>>>>>> my $member_attributes = $this_homology->
>>>>>>>>>>> get_all_Member_Attribute();
>>>>>>>>>>> foreach my $this_mem_attr (@$member_attributes) {
>>>>>>>>>>> my ($this_member, $this_attribute) =
>>>>>>>>>>> @$this_mem_attr;
>>>>>>>>>>> print $this_member->genome_db->name, " ",
>>>>>>>>>>> $this_member->source_name, " ",
>>>>>>>>>>> $this_member->stable_id, "\n";
>>>>>>>>>>> }
>>>>>>>>>>> print "\n";
>>>>>>>>>>> }
>>>>>>>>>>>
>>>>>>>>>>> ==========================================
>>>>>>>>>>>
>>>>>>>>>>> From the list:
>>>>>>>>>>> use Bio::EnsEMBL::Registry;
>>>>>>>>>>> Bio::EnsEMBL::Registry->load_registry_from_db(
>>>>>>>>>>> -host => 'ensembldb.ensembl.org',
>>>>>>>>>>> -user => 'anonymous',
>>>>>>>>>>> -port => 5306);
>>>>>>>>>>> my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
>>>>>>>>>>> 'Multi','compara','Member');
>>>>>>>>>>>
>>>>>>>>>>> # fetch a Member
>>>>>>>>>>> # get the MemberAdaptor
>>>>>>>>>>> my $member_adaptor =
>>>>>>>>>>> Bio::EnsEMBL::Registry->get_adaptor('Multi','compara','Member');
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> # fetch a Memmy $member =
>>>>>>>>>>> $member_adaptor->fetch_by_source_stable_id('ENSEMBLPROTEIN','ENSG00000004059');
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> my $member =
>>>>>>>>>>> $member_adaptor->fetch_by_source_stable_id('ENSEMBLPEP','ENSDARP00000103634');
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> # print out some information about the Member
>>>>>>>>>>> print $member->description, "\n";
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> my $homology_adaptor =
>>>>>>>>>>> Bio::EnsEMBL::Registry->get_adaptor('Multi',
>>>>>>>>>>> 'compara', 'Homology');
>>>>>>>>>>> my $homologies =
>>>>>>>>>>> $homology_adaptor->fetch_all_by_Member($member);
>>>>>>>>>>>
>>>>>>>>>>> # That will return a reference to an array with all
>>>>>>>>>>> homologies(orthologues in
>>>>>>>>>>> # other species and paralogues in the same one)
>>>>>>>>>>> # Then for each homology, you can get all the Members
>>>>>>>>>>> implicated
>>>>>>>>>>>
>>>>>>>>>>> foreach my $homology (@{$homologies}) {
>>>>>>>>>>> # You will find different kind of description
>>>>>>>>>>> # UBRH, MBRH, RHS, YoungParalogues
>>>>>>>>>>> # see ensembl-compara/docs/docs/schema_doc.html for more
>>>>>>>>>>> details
>>>>>>>>>>>
>>>>>>>>>>> print $homology->description," ", $homology->subtype,"\n";
>>>>>>>>>>> # And if they are defined dN and dS related values
>>>>>>>>>>> print " dn ", $homology->dn,"\n";
>>>>>>>>>>> print " ds ", $homology->ds,"\n";
>>>>>>>>>>> print " dnds_ratio ", $homology->dnds_ratio,"\n";
>>>>>>>>>>> }
>>>>>>>>>>>
>>>>>>>>>>> my $homology = $homologies->[0];
>>>>>>>>>>> # take one of the homologies and lookinto it
>>>>>>>>>>>
>>>>>>>>>>> foreach my $member_attribute
>>>>>>>>>>> (@{$homology->get_all_Member_Attribute}) {
>>>>>>>>>>>
>>>>>>>>>>> # for each Member, you get information on the Member
>>>>>>>>>>> specifically
>>>>>>>>>>> and in
>>>>>>>>>>> # relation to the homology relation via Attribute object
>>>>>>>>>>>
>>>>>>>>>>> my ($member, $attribute) = @{$member_attribute};
>>>>>>>>>>> print (join " ", map { $member->$_ } qw(stable_id
>>>>>>>>>>> taxon_id))."\n";
>>>>>>>>>>> print (join " ", map { $attribute->$_ } qw(perc_id
>>>>>>>>>>> perc_posperc_cov))."\n";
>>>>>>>>>>>
>>>>>>>>>>> }
>>>>>>>>>>> ====================================================
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> James Blackshaw
>>>>>>>>>>> PhD Student
>>>>>>>>>>> MRC Mitochondrial Biology Unit
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Dev mailing list Dev at ensembl.org<mailto:Dev at ensembl.org>
>>>>>>>>>>> List admin (including subscribe/unsubscribe):
>>>>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Dev mailing listDev at ensembl.org<mailto:Dev at ensembl.org>
>>>>>>>>>> List admin (including
>>>>>>>>>> subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>>
>>>>>>>>>> Ensembl Blog:http://www.ensembl.info/
>>>>>>>>> --
>>>>>>>>> Javier Herrero, PhD
>>>>>>>>> Ensembl Compara Project Leader
>>>>>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>>>>>> Wellcome Trust Genome Campus, Hinxton
>>>>>>>>> Cambridge - CB10 1SD - UK
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Dev mailing listDev at ensembl.org<mailto:Dev at ensembl.org>
>>>>>>>>> List admin (including
>>>>>>>>> subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>>
>>>>>>>>> Ensembl Blog:http://www.ensembl.info/
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>> List admin (including subscribe/unsubscribe):
>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing list Dev at ensembl.org
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>>>> Ensembl Blog: http://www.ensembl.info/
>>> ---
>>> Andrew Yates Ensembl Core Software Project Leader
>>> EMBL-EBI Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK http://www.ensembl.org/
>>>
>>
>
>
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> Dev mailing list Dev at ensembl.org
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>
--
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
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